1

[1] 1

Full table

The GFP/iPSC/RFP columns are the number of peaks with the motif associated (by distance) to the gene

Ratio is GFP/RFP

Delta is GFP - RFP

If log2FC is positive, then the expression of the gene is higher in RPE vs iPSC

TF_gene_stats %>% dplyr::select(motif = motif_core, Gene:padj__RPE_vs_iPSC, motif_full = motif) %>% DT::datatable( filter = list(position = 'top', clear = FALSE),
                                                                                                                   extensions = 'Buttons', options = list(
                                                                                                                     lengthMenu = list(c(5, 15, 30, 60, 100, -1), list('5', '15', '30', '60', '100', 'All')),
                                                                                                                     dom = 'Bfrtip',
                                                                                                                     buttons = c('copy', 'csv', 'excel', 'pageLength')
                                                                                                                   ))
It seems your data is too big for client-side DataTables. You may consider server-side processing: https://rstudio.github.io/DT/server.htmlIt seems your data is too big for client-side DataTables. You may consider server-side processing: https://rstudio.github.io/DT/server.html

count number of genes associated with each TFBS

TF_gene_stats %>% group_by(motif_core) %>% summarise(count = n(), Gene = paste(Gene, collapse = ',') ) %>% arrange(-count) %>% DT::datatable()

most common genes associated with TF

TF_gene_stats %>% group_by(Gene) %>% summarise(count = n(), motif = paste(motif_core, collapse=',')) %>% arrange(-count) %>%  DT::datatable( filter = list(position = 'top', clear = FALSE))

First attempt at network

No more than 10 genes assigned to a single TF

Red are the homer ID’ed TF(BS)

Pink are genes labelled as TF by GO term (but not ID’ed by homer)

If you hover you get the log2FC

You can zoom in and out

Clicking on a node gives you all the other nodes within 2 edges

library(visNetwork)
TF_gene_stats_n <- TF_gene_stats %>% 
  # filter(!grepl('GATA', motif_core)) %>% 
  group_by(motif_core) %>% 
  top_n(10, delta) %>% # no more than n by tF
  #filter(!Gene %in% c('FZD8','OPCML','PFKP','NRIP1','TSHZ3', 'SOX6')) %>% # trimming out most common genes between TF
  ungroup()
TF <- TF_gene_stats_n %>%
  distinct(motif_core) %>%
  rename(label = motif_core)
genes <- TF_gene_stats_n %>%
  distinct(Gene) %>%
  rename(label = Gene)
nodes <- full_join(TF, genes, by = "label") %>%  arrange(label) %>% rowid_to_column("id") %>% mutate(group = case_when(label %in% TF$label ~ 'TF', 
                                                                                                                       TRUE ~ 'Gene'),
                                                                                                     shape = 'box') %>% 
  left_join(., expression %>% 
              select(Gene, value = log2FoldChange__RPE_vs_iPSC, goTF = TF) %>% 
              unique(), by = c("label" = "Gene")) %>% 
  mutate(title = paste0('Gene: ', label, '<br>log2FC: ', round(value,2))) %>% 
  mutate(group = case_when(group == 'TF' ~ 'TF',
                           goTF == 'Yes' ~ 'goTF',
                           TRUE ~ 'Gene'))
edges <- TF_gene_stats_n %>%  
  select(TF = motif_core, Gene, weight = log2FoldChange__RPE_vs_iPSC) %>% 
  unique() %>% 
  left_join(nodes, by = c("TF" = "label")) %>% 
  rename(from = id) %>% 
  left_join(nodes, by = c("Gene" = "label")) %>% 
  rename(to = id) %>% 
  ungroup() %>% 
  select(from, to, weight) 
visNetwork(nodes, edges, height = "700px", width = "100%") %>% 
  visGroups(groupname = 'TF', color='red') %>% 
  visGroups(groupname = 'goTF', color = 'pink') %>% 
  visOptions(highlightNearest = list(enabled = T, degree = 2),
             nodesIdSelection = TRUE) %>% 
  visPhysics(stabilization = TRUE) %>% 
  visEdges(smooth = FALSE) %>% 
  visInteraction(navigationButtons = TRUE)
---
title: Analysis of TFBS <-> Gene Interaction via Peak
author: David McGaughey
date: '`r format(Sys.Date(), "%Y-%m-%d")`'
output: 
  html_notebook:
    theme: flatly
    toc: true
---

```{r}
library(tidyverse)
peak <- read_tsv('/Volumes/data/projects/nei/hufnagel/iPSC_RPE_ATAC_Seq/peak_full/all_common_peaks.blackListed.narrowPeak.closestTSS__interesting_homer_motif.bed.gz', col_names = F)
expression <- read_csv('~/git/ipsc_rpe_RNA-seq/data/lsTPM_by_Line_with_Diff_Exp.tsv')

colnames(peak) <- c('chrom','start','stop','type','macs2_score','strand','thickStart','thickStop','RGB','Distance_to_Gene','Gene','Description','chrom_motif','start_motif','stop_motif','motif','motif_score','strand_motif')

motifs <- peak$motif %>% unique()

# create gene centric info on peak/motif and differential gene expression iPSC <-> RPE
grouped_stats <- list()

for (i in motifs){
  out <- peak %>% 
    filter(!is.na(Gene)) %>% # remove NA genes where the peak didn't get a match (no genes within 500kb of a peak)
    filter(motif == i) %>% # only retain the motif TFBS homer hits
    group_by(type, chrom, start, stop, Gene) %>% # group by GFP/RFP,iPSC, the macs2 peak, and the gene
    summarise(Num_TFBS_motifs=n()) %>%  # count total number of motifs
    group_by(type, Gene) %>% # group now by GFP/RFP/IPSC and gene
    summarise(Total_TFBS_motifs = sum(Num_TFBS_motifs), Num_Peaks = n()) %>% # now add num of peaks near gene
    select(type, Gene, Total_TFBS_motifs, Num_Peaks)
  grouped_stats[[i]] <- out
  print(i)
}

# further cut down to most interesting genes by differential peak activity and 
# expression by TF

TF_gene_stats_list <- list()

for (i in motifs){
  
  # ID differentially peak activity around genes for a TF
  out <- grouped_stats[[i]] %>% select(-Total_TFBS_motifs) %>% 
    spread(type, Num_Peaks)
  out[is.na(out)] <- 0
  out <- out %>% 
    mutate(ratio = GFP/iPSC, delta = GFP - iPSC) %>% 
    arrange(-delta) %>% 
    left_join(expression %>% 
                select(Gene, log2FoldChange__RPE_vs_iPSC, padj__RPE_vs_iPSC) %>% 
                unique()) %>% 
    filter(!is.na(padj__RPE_vs_iPSC), 
           abs(log2FoldChange__RPE_vs_iPSC) > 1, 
           padj__RPE_vs_iPSC < 0.01) %>% 
    filter(delta > 1, ratio > 1.5) # only keep 
  TF_gene_stats_list[[i]] <- out
  print(i)
}

TF_gene_stats <- bind_rows(TF_gene_stats_list, .id = 'motif') %>% rowwise() %>% mutate(motif_core = toupper(gsub('\\(.*|11-GGGTGTGT,BestGuess:','',motif))) %>% ungroup()
```

# Full table
The GFP/iPSC/RFP columns are the number of peaks with the motif associated (by distance) to the gene

Ratio is GFP/RFP

Delta is GFP - RFP

If log2FC is positive, then the expression of the gene is higher in RPE vs iPSC
```{r}
TF_gene_stats %>% dplyr::select(motif = motif_core, Gene:padj__RPE_vs_iPSC, motif_full = motif) %>% DT::datatable( filter = list(position = 'top', clear = FALSE),
                                                                                                                   extensions = 'Buttons', options = list(
                                                                                                                     lengthMenu = list(c(5, 15, 30, 60, 100, -1), list('5', '15', '30', '60', '100', 'All')),
                                                                                                                     dom = 'Bfrtip',
                                                                                                                     buttons = c('copy', 'csv', 'excel', 'pageLength')
                                                                                                                   ))
```

# count number of genes associated with each TFBS
```{r}
TF_gene_stats %>% group_by(motif_core) %>% summarise(count = n(), Gene = paste(Gene, collapse = ',') ) %>% arrange(-count) %>% DT::datatable()
```
# most common genes associated with TF
```{r}
TF_gene_stats %>% group_by(Gene) %>% summarise(count = n(), motif = paste(motif_core, collapse=',')) %>% arrange(-count) %>%  DT::datatable( filter = list(position = 'top', clear = FALSE))
```

# First attempt at network
No more than 10 genes assigned to a single TF

Red are the homer ID'ed TF(BS)

Pink are genes labelled as TF by GO term (but not ID'ed by homer)

If you hover you get the log2FC

You can zoom in and out

Clicking on a node gives you all the other nodes within 2 edges
```{r, fig.height=6, fig.width=6}
library(visNetwork)
TF_gene_stats_n <- TF_gene_stats %>% 
  # filter(!grepl('GATA', motif_core)) %>% 
  group_by(motif_core) %>% 
  top_n(10, delta) %>% # no more than n by tF
  #filter(!Gene %in% c('FZD8','OPCML','PFKP','NRIP1','TSHZ3', 'SOX6')) %>% # trimming out most common genes between TF
  ungroup()

TF <- TF_gene_stats_n %>%
  distinct(motif_core) %>%
  rename(label = motif_core)

genes <- TF_gene_stats_n %>%
  distinct(Gene) %>%
  rename(label = Gene)

nodes <- full_join(TF, genes, by = "label") %>%  arrange(label) %>% rowid_to_column("id") %>% mutate(group = case_when(label %in% TF$label ~ 'TF', 
                                                                                                                       TRUE ~ 'Gene'),
                                                                                                     shape = 'box') %>% 
  left_join(., expression %>% 
              select(Gene, value = log2FoldChange__RPE_vs_iPSC, goTF = TF) %>% 
              unique(), by = c("label" = "Gene")) %>% 
  mutate(title = paste0('Gene: ', label, '<br>log2FC: ', round(value,2))) %>% 
  mutate(group = case_when(group == 'TF' ~ 'TF',
                           goTF == 'Yes' ~ 'goTF',
                           TRUE ~ 'Gene'))




edges <- TF_gene_stats_n %>%  
  select(TF = motif_core, Gene, weight = log2FoldChange__RPE_vs_iPSC) %>% 
  unique() %>% 
  left_join(nodes, by = c("TF" = "label")) %>% 
  rename(from = id) %>% 
  left_join(nodes, by = c("Gene" = "label")) %>% 
  rename(to = id) %>% 
  ungroup() %>% 
  select(from, to, weight) 

visNetwork(nodes, edges, height = "700px", width = "100%") %>% 
  visGroups(groupname = 'TF', color='red') %>% 
  visGroups(groupname = 'goTF', color = 'pink') %>% 
  visOptions(highlightNearest = list(enabled = T, degree = 2),
             nodesIdSelection = TRUE) %>% 
  visPhysics(stabilization = TRUE) %>% 
  visEdges(smooth = FALSE) %>% 
  visInteraction(navigationButtons = TRUE)
```

